[gmx-users] GMX hbond

[Dhumal, Nilesh]

I tried, didn't find the proper answer. I run the simulation using Gromacs 4.5 version and used g_hbond successfully.  Could not find out why its not working using gmx hbond.

Nilesh

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
> Hello Gromacs users,
>
>
> I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 5.1.4. I did following steps
>
> mx hbond -f traj.trr -s md.tpr -n index.ndx -ac
>
> Reading file md.tpr, VERSION 5.1.4 (single precision)
> Specify 2 groups to analyze:
> Group     0 (         System) has  2560 elements
> Group     1 (          Other) has  2432 elements
> Group     2 (            EMI) has  2432 elements
> Group     3 (             CL) has   128 elements
> Group     4 (            Ion) has   128 elements
> Group     5 (            EMI) has  2432 elements
> Group     6 (             CL) has   128 elements
> Group     7 (              C) has   128 elements
> Group     8 (             C2) has   128 elements
> Group     9 (             C4) has   128 elements
> Group    10 (             H9) has   128 elements
> Group    11 (            H10) has   128 elements
> Group    12 (            H11) has   128 elements
> Group    13 (             CL) has   128 elements
> Group    14 (             ch) has   256 elements
> Group    15 (             ch) has     3 elements
> Group    16 (             O1) has     2 elements
> Select a group: 14
> Selected 14: 'ch'
> Select a group: 13
> Selected 13: 'CL'
> Checking for overlap in atoms between ch and CL
> Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
> Found 0 donors and 0 acceptors
> Making hbmap structure...done.
> No Donors or Acceptors found
>
> -------------------------------------------------------
> Program gmx hbond, VERSION 5.1.4
> Source code file: /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, l                                                                                                              ine: 3984
>
> Fatal error:
> Nothing to be done
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Group 14 is list of donor hydrogen (eg. 4(donor)     11(hydrogen)) and group is list of acceptors . Why donors and acceptors are zero.

Have you tried Googling the error? The first result has the answer...

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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